Haou Airen got me crying a lot. ;~; So did the "Deep Love" series.
And a few of Taamo's works like Onegai sensei's 3rd story, Taiyou no ie , koi tsukiyo no himegoto.
One Piece has made me cry too. [Though I don't read the manga anymore.]

There is allot of Yuri manga that made me teary eyed or start to cry because so much Yuri manga is made to be tragic (written that way on purpose of course). Since you are speaking only of manga, for a well known title I would say 'Sasameki Koto (Whispered Words)' Manga. I really got into the relationship between Kazama and Sumi-chan, first in knowing from real life how it is to Love a girl you probably can never be with; and then later in the story how much Sumi deeply Loved Ushio; and of course another somewhat tragic Yuri ending which I did not like at all. Like many fans I needed a happy ending full of Yuri/Lesbian bliss. So, yes, if I watch the anime and read all the volumes of the manga (final volume 9 is out and pictured below), then before I get done the tears start flowing. Oh well, I'm a crybaby.

I think I'm wired differently than most people. I love Shounen but have a rather strong dislike for most Shoujo titles. So. The manga that made me cry, the ones that I really remember what set those tears off are Eyeshield 21 and One Piece. I'm pretty sure other manga titles made me cry a bit, but I just can't remember at the moment.

For the record, I have read Eyeshield 21 TWO times from first to the finish and I cried both times. So much feels. That guy who wrote it is genius, and that manga-ka is epic.